9SH9

Thermus thermophilus asparaginyl-tRNA synthetase dimer with bound ATP

Summary for 9SH9

• Entry DOI: 10.2210/pdb9sh9/pdb
• Descriptor: Asparagine--tRNA ligase, MAGNESIUM ION, ADENOSINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: rna binding protein enzyme, synthetises asparaginyl-adenylate from asparagine and atp, translation
• Biological source: Thermus thermophilus HB8
• Total number of polymer chains: 2
• Total formula weight: 102877.90

Authors

Cusack, S.,Seignovert, L.,Leberman, R.,Berthet-Colominas, C. (deposition date: 2025-08-25, release date: 2025-09-17)

Primary citation

Berthet-Colominas, C.,Seignovert, L.,Haertlein, M.,Grotli, M.,Cusack, S.,Leberman, R.
The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid.
EMBO J, 17:2947-2960, 1998

PubMed Abstract: The crystal structure of Thermus thermophilus asparaginyl-tRNA synthetase has been solved by multiple isomorphous replacement and refined at 2.6 A resolution. This is the last of the three class IIb aminoacyl-tRNA synthetase structures to be determined. As expected from primary sequence comparisons, there are remarkable similarities between the tertiary structures of asparaginyl-tRNA synthetase and aspartyl-tRNA synthetase, and most of the active site residues are identical except for three key differences. The structure at 2.65 A of asparaginyl-tRNA synthetase complexed with a non-hydrolysable analogue of asparaginyl-adenylate permits a detailed explanation of how these three differences allow each enzyme to discriminate between their respective and very similar amino acid substrates, asparagine and aspartic acid. In addition, a structure of the complex of asparaginyl-tRNA synthetase with ATP shows exactly the same configuration of three divalent cations as previously observed in the seryl-tRNA synthetase-ATP complex, showing that this a general feature of class II synthetases. The structural similarity of asparaginyl- and aspartyl-tRNA synthetases as well as that of both enzymes to the ammonia-dependent asparagine synthetase suggests that these three enzymes have evolved relatively recently from a common ancestor.

PubMed: 9582288
DOI: 10.1093/emboj/17.10.2947

Experimental method

X-RAY DIFFRACTION (2.95 Å)